# Why denoising itself on DADA2 is filtering some reads?
**URL:** https://forum.qiime2.org/t/why-denoising-itself-on-dada2-is-filtering-some-reads/15803
**Category:** User Support
**Tags:** dada2
**Created:** [July 22, 2020, 3:09am UTC](https://forum.qiime2.org/t/why-denoising-itself-on-dada2-is-filtering-some-reads/15803 "2020-07-22T03:09:52Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@vheidrich](https://forum.qiime2.org/u/vheidrich)
#### Post date: [July 22, 2020, 3:09am UTC](https://forum.qiime2.org/t/why-denoising-itself-on-dada2-is-filtering-some-reads/15803/1 "2020-07-22T03:09:52Z")
Hi,
I was taking a look on this [reply](https://forum.qiime2.org/t/using-dada2-losing-50-of-reads-after-filtering-and-80-of-reads-by-the-end/12745/2) by @FrancineMarques and now I am wondering why reads are being filtered on denoising step from DADA2? ("denoised" columns from stats file)
As far as I know, this did not happen in early implementations of qiime dada2 plugin (am I right?)
Thank you
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [July 27, 2020, 3:44pm UTC](https://forum.qiime2.org/t/why-denoising-itself-on-dada2-is-filtering-some-reads/15803/2 "2020-07-27T15:44:44Z")
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [July 27, 2020, 8:42pm UTC](https://forum.qiime2.org/t/why-denoising-itself-on-dada2-is-filtering-some-reads/15803/3 "2020-07-27T20:42:14Z")
Hi @vheidrich!
> [@vheidrich](#):
>
> now I am wondering why reads are being filtered on denoising step from DADA2?
Have you had a chance to read the DADA2 paper?
> **[DADA2: High resolution sample inference from Illumina amplicon data](https://pmc.ncbi.nlm.nih.gov/articles/PMC4927377/)**
>
> We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock ...
Not all reads are able to be denoised (for reasons discussed in the paper above), which is why the step might indicate a decrease in read count.
> [@vheidrich](#):
>
> this did not happen in early implementations of qiime dada2 plugin (am I right?)
No, I think that has been the case for as long as this plugin has existed (someone please correct me if I am wrong). The denoising summary is a bit newer than the plugin itself, though, but I think it is 2 or 3 years old now at this point.
:qiime2:
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [July 27, 2020, 8:42pm UTC](https://forum.qiime2.org/t/why-denoising-itself-on-dada2-is-filtering-some-reads/15803/4 "2020-07-27T20:42:17Z")
---
### Author:  [@vheidrich](https://forum.qiime2.org/u/vheidrich)
#### Post date: [July 27, 2020, 10:33pm UTC](https://forum.qiime2.org/t/why-denoising-itself-on-dada2-is-filtering-some-reads/15803/5 "2020-07-27T22:33:35Z")
Hi @thermokarst! Thank you very much for your reply
Some days ago, after some detective work, I found the answer for my question in another [place](https://github.com/benjjneb/dada2/issues/494#issuecomment-397110430). Apparently, there wasn't read loss in denoising step in earlier dada2 versions, including [the one](https://forum.qiime2.org/t/is-the-dada2-plugin-version-installed-in-qiime-2019-1-suitable-for-pacbio-16s-rrna-analysis/9191) implemented in qiime2-2019.1. Since dada2 version 1.8, a quite irrelevant number of reads might be excluded during denoising.
Previous behavior ("correct everything") can be recovered in R implementation of dada2. I am afraid we can't force current QIIME2 implementation of dada2 to "correct everything", right?
Thanks again
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [August 28, 2020, 4:34am UTC](https://forum.qiime2.org/t/why-denoising-itself-on-dada2-is-filtering-some-reads/15803/6 "2020-08-28T04:34:16Z")
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.